Inside the Little Plastic Castle

Murderbot 1.0 and ART made a software spin off of Murderbot designed to infect and kill enemy systems. It had a lot of Murderbot's memories and some of its functionality, plus some system fighting skills ART added. It wrote the helpme.file from Murderbot's memories to give to a completely seperate SecUnit, Three, so that Three would understand why it should help free ART's crew.

So you have:
Murderbot 1.0: regular secunit we've had all along.
Murderbot 2.0: Killware file with Murderbot memories, who wrote the helpme.file. 2.0 dies defeating the Remnant-infected control system.
Three: Different secunit entirely.

In terms of timeline:
1.0 for most of the story.
Art and 1.0 make 2.0 right before 1.0 goes to the space station.
2.0 generates the helpme.file from it and 1.0's memories right when it meets Three for the first time.

That the helpme.file is woven back through 1.0's PoV is just an indication that 2.0 sent basically everything we've read in the book so far to Three. Is my understanding anyway.